Class ProbeSet

Description

A simple class that contains the PM and MM data for a probe set from one or more samples.

Objects from the Class

Objects can be created by applying the method probeset to instances of AffyBatch.

Slots

id:

Object of class "character" containing the probeset ID.

pm:

Object of class "matrix" containing the PM intensities. Columns represent samples and rows the different probes.

mm:

Object of class "matrix" containing the MM intensities.

Methods

colnames

signature(x = "ProbeSet"): the column names of the pm matrices which are the sample names

express.summary.stat

signature(x = "ProbeSet", pmcorrect = "character", summary = "character"): applies a summary statistic to the probe set.

sampleNames

signature(object = "ProbeSet"): the column names of the pm matrices which are the sample names.

Note

More details are contained in the vignette.

See Also

probeset, AffyBatch-class

Examples

if (require(affydata)) {
  data(Dilution)
  ps <- probeset(Dilution, geneNames(Dilution)[1:2])
  names(ps)
  print(ps[[1]])
}

Results

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> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/ProbeSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ProbeSet-class
> ### Title: Class ProbeSet
> ### Aliases: ProbeSet-class mm,ProbeSet-method mm<-,ProbeSet,matrix-method
> ###   pm<-,ProbeSet,matrix-method pm,ProbeSet-method show,ProbeSet-method
> ###   barplot,ProbeSet-method colnames,ProbeSet-method
> ###   express.summary.stat,ProbeSet,character,character-method
> ###   sampleNames,ProbeSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+   ps <- probeset(Dilution, geneNames(Dilution)[1:2])
+   names(ps)
+   print(ps[[1]])
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

ProbeSet object:
  id=1000_at
  pm= 16 probes x  4  chips
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>